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PIWI-interacting RNAs: small RNAs with big functions

Abstract

In animals, PIWI-interacting RNAs (piRNAs) of 21–35 nucleotides in length silence transposable elements, regulate gene expression and fight viral infection. piRNAs guide PIWI proteins to cleave target RNA, promote heterochromatin assembly and methylate DNA. The architecture of the piRNA pathway allows it both to provide adaptive, sequence-based immunity to rapidly evolving viruses and transposons and to regulate conserved host genes. piRNAs silence transposons in the germ line of most animals, whereas somatic piRNA functions have been lost, gained and lost again across evolution. Moreover, most piRNA pathway proteins are deeply conserved, but different animals employ remarkably divergent strategies to produce piRNA precursor transcripts. Here, we discuss how a common piRNA pathway allows animals to recognize diverse targets, ranging from selfish genetic elements to genes essential for gametogenesis.

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Fig. 1: Genomic sources of piRNAs.
Fig. 2: Type I piRNA biogenesis in Caenorhabditis elegans.
Fig. 3: piRNA biogenesis in most animals.
Fig. 4: The preference of PIWI proteins for t1A targets is one of the sources of the g1U bias of piRNAs.
Fig. 5: Diverse functions of piRNAs.

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References

  1. Aravin, A. et al. A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442, 203–207 (2006).

    CAS  PubMed  Google Scholar 

  2. Girard, A., Sachidanandam, R., Hannon, G. J. & Carmell, M. A. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature 442, 199–202 (2006).

    PubMed  Google Scholar 

  3. Vagin, V. V. et al. A distinct small RNA pathway silences selfish genetic elements in the germline. Science 313, 320–324 (2006). This study demonstrates that piRNAs are distinct from miRNAs and siRNAs and form a novel class of Dicer-independent, PIWI protein-associated small silencing RNAs present in the fly ovary and derived from single-stranded RNA and bearing a chemically modified 3' end.

    CAS  PubMed  Google Scholar 

  4. Lau, N. C. et al. Characterization of the piRNA complex from rat testes. Science 313, 363–367 (2006).

    CAS  PubMed  Google Scholar 

  5. Grivna, S. T., Beyret, E., Wang, Z. & Lin, H. A novel class of small RNAs in mouse spermatogenic cells. Genes Dev. 20, 1709–1714 (2006). References 1, 2, 4 and 5 report the discovery of piRNAs in mouse, rat and human germ cells and that mammalian PIWI proteins are required for male fertility.

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Saito, K. et al. Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome. Genes Dev. 20, 2214–2222 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Houwing, S. et al. A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in zebrafish. Cell 129, 69–82 (2007).

    CAS  PubMed  Google Scholar 

  8. Batista, P. J. et al. PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans. Mol. Cell 31, 67–78 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Das, P. P. et al. Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Mol. Cell 31, 79–90 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Horwich, M. D. et al. The Drosophila RNA methyltransferase, DmHen1, modifies germline piRNAs and single-stranded siRNAs in RISC. Curr. Biol. 17, 1265–1272 (2007).

    CAS  PubMed  Google Scholar 

  11. Saito, K. et al. Pimet, the Drosophila homolog of HEN1, mediates 2ʹ-O-methylation of Piwi-interacting RNAs at their 3ʹ ends. Genes Dev. 21, 1603–1608 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Ohara, T. et al. The 3ʹ termini of mouse piwi-interacting RNAs are 2ʹ-O-methylated. Nat. Struct. Mol. Biol. 14, 349–350 (2007).

    CAS  PubMed  Google Scholar 

  13. Montgomery, T. A. et al. PIWI associated siRNAs and piRNAs specifically require the Caenorhabditis elegans HEN1 ortholog henn-1. PLOS Genet. 8, e1002616 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Kirino, Y. & Mourelatos, Z. Mouse Piwi-interacting RNAs are 2ʹ-O-methylated at their 3ʹ termini. Nat. Struct. Mol. Biol. 14, 347–348 (2007). References 10–14 provide evidence that piRNAs are 2ʹ-O-methylated at their 3ʹ termini and that the protein Hen1 in flies or its orthologues in other animals catalyse this modification.

    CAS  PubMed  Google Scholar 

  15. Kirino, Y. & Mourelatos, Z. The mouse homolog of HEN1 is a potential methylase for Piwi-interacting RNAs. RNA 13, 1397–1401 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Lim, S. L. et al. HENMT1 and piRNA stability are required for adult male germ cell transposon repression and to define the spermatogenic program in the mouse. PLOS Genet. 11, e1005620 (2015).

    PubMed  PubMed Central  Google Scholar 

  17. Billi, A. C. et al. The Caenorhabditis elegans HEN1 ortholog, HENN-1, methylates and stabilizes select subclasses of germline small RNAs. PLOS Genet. 8, e1002617 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Kamminga, L. M. et al. Differential impact of the HEN1 homolog HENN-1 on 21U and 26G RNAs in the germline of Caenorhabditis elegans. PLOS Genet. 8, e1002702 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Kamminga, L. M. et al. Hen1 is required for oocyte development and piRNA stability in zebrafish. EMBO J. 29, 3688–3700 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Brennecke, J. et al. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128, 1089–1103 (2007). This study shows that fly piRNA-producing loci are graveyards of transposon remnants dedicated to recording the history of transposon invasion in an animal.

    CAS  PubMed  Google Scholar 

  21. Ruby, J. G. et al. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127, 1193–1207 (2006).

    CAS  PubMed  Google Scholar 

  22. Cecere, G., Zheng, G. X., Mansisidor, A. R., Klymko, K. E. & Grishok, A. Promoters recognized by forkhead proteins exist for individual 21U-RNAs. Mol. Cell 47, 734–745 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Gu, W. et al. CapSeq and CIP-TAP map 5ʹ ends of Pol II transcripts and reveal capped-small RNAs as C. elegans piRNA precursors. Cell 151, 1488–1500 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Fu, Y. et al. The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology. eLife 7, e31628 (2018).

    PubMed  PubMed Central  Google Scholar 

  25. Kawaoka, S. et al. The Bombyx ovary-derived cell line endogenously expresses PIWI/PIWI-interacting RNA complexes. RNA 15, 1258–1264 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Lewis, S. H. et al. Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements. Nat. Ecol. Evol. 2, 174–181 (2018). This study shows that somatic piRNAs targeting transposons or viruses are nearly ubiquitously present in arthropods.

    PubMed  Google Scholar 

  27. Li, X. Z. et al. An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes. Mol. Cell 50, 67–81 (2013). This study shows that, in mammals and birds, the transcription of both pachytene piRNA-producing loci and several piRNA biogenesis genes at the onset of meiosis is initiated by the conserved transcription factor A-MYB, the master regulator of male meiosis.

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Aravin, A. A., Sachidanandam, R., Girard, A., Fejes-Toth, K. & Hannon, G. J. Developmentally regulated piRNA clusters implicate MILI in transposon control. Science 316, 744–747 (2007).

    CAS  PubMed  Google Scholar 

  29. Aravin, A. A. et al. A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol. Cell 31, 785–799 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Kuramochi-Miyagawa, S. et al. DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes. Genes Dev. 22, 908–917 (2008). References 29 and 30 are the first to demonstrate that mammalian fetal piRNAs repress transposons transcriptionally by directing DNA methylation.

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Aravin, A. A. et al. Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Curr. Biol. 11, 1017–1027 (2001). This study is the first to identify piRNAs.

    CAS  PubMed  Google Scholar 

  32. Belloni, M., Tritto, P., Bozzetti, M. P., Palumbo, G. & Robbins, L. G. Does Stellate cause meiotic drive in Drosophila melanogaster? Genetics 161, 1551–1559 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Bozzetti, M. P. et al. The Ste locus, a component of the parasitic cry-Ste system of Drosophila melanogaster, encodes a protein that forms crystals in primary spermatocytes and mimics properties of the beta subunit of casein kinase 2. Proc. Natl Acad. Sci. USA 92, 6067–6071 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Hardy, R. W. et al. Cytogenetic analysis of a segment of the Y chromosome of Drosophila melanogaster. Genetics 107, 591–610 (1984).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Livak, K. J. Organization and mapping of a sequence on the Drosophila melanogaster X and Y chromosomes that is transcribed during spermatogenesis. Genetics 107, 611–634 (1984).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Livak, K. J. Detailed structure of the Drosophila melanogaster stellate genes and their transcripts. Genetics 124, 303–316 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Meyer, G. F., Hess, O. & Beermann, W. Phasenspezifische Funktionsstrukturen in Spermatocytenkernen von Drosophila melanogaster und Ihre Abhängigkeit vom Y-Chromosom [German]. Chromosoma 12, 676 (1961).

    CAS  PubMed  Google Scholar 

  38. Aravin, A. A. et al. Dissection of a natural RNA silencing process in the Drosophila melanogaster germ line. Mol. Cell. Biol. 24, 6742–6750 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Prud’homme, N., Gans, M., Masson, M., Terzian, C. & Bucheton, A. Flamenco, a gene controlling the gypsy retrovirus of Drosophila melanogaster. Genetics 139, 697–711 (1995).

    PubMed  PubMed Central  Google Scholar 

  40. Sarot, E., Payen-Groschene, G., Bucheton, A. & Pelisson, A. Evidence for a piwi-dependent RNA silencing of the gypsy endogenous retrovirus by the Drosophila melanogaster flamenco gene. Genetics 166, 1313–1321 (2004). References 39 and 40 identify the transposon-silencing gene flamenco in flies and provide evidence that it does not encode a protein but instead produces piRNAs that repress the endogenous retrovirus gypsy.

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Sarkies, P. et al. Ancient and novel small RNA pathways compensate for the loss of piRNAs in multiple independent nematode lineages. PLOS Biol. 13, e1002061 (2015).

    PubMed  PubMed Central  Google Scholar 

  42. Grimson, A. et al. Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 455, 1193–1197 (2008).

    CAS  PubMed  Google Scholar 

  43. Mondal, M., Klimov, P. & Flynt, A. S. Rewired RNAi-mediated genome surveillance in house dust mites. PLOS Genet. 14, e1007183 (2018).

    PubMed  PubMed Central  Google Scholar 

  44. Johnson, A. D., Richardson, E., Bachvarova, R. F. & Crother, B. I. Evolution of the germ line-soma relationship in vertebrate embryos. Reproduction 141, 291–300 (2011).

    CAS  PubMed  Google Scholar 

  45. Brennecke, J. et al. An epigenetic role for maternally inherited piRNAs in transposon silencing. Science 322, 1387–1392 (2008). This study shows that maternally deposited piRNAs confer an adaptive piRNA response in insects by initiating transposon silencing in the germ line of progeny.

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Kawaoka, S. et al. Zygotic amplification of secondary piRNAs during silkworm embryogenesis. RNA 17, 1401–1407 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. de Vanssay, A. et al. Paramutation in Drosophila linked to emergence of a piRNA-producing locus. Nature 490, 112–115 (2012).

    PubMed  Google Scholar 

  48. Le Thomas, A. et al. Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing. Genes Dev. 28, 1667–1680 (2014).

    PubMed  PubMed Central  Google Scholar 

  49. Le Thomas, A., Marinov, G. & Aravin, A. A. A trans-generational process defines piRNA biogenesis in Drosophila virilis. Cell Rep. 8, 1617–1623 (2014).

    PubMed  PubMed Central  Google Scholar 

  50. Ninova, M., Griffiths-Jones, S. & Ronshaugen, M. Abundant expression of somatic transposon-derived piRNAs throughout Tribolium castaneum embryogenesis. Genome Biol. 18, 184 (2017).

    PubMed  PubMed Central  Google Scholar 

  51. Kidwell, M. G. & Kidwell, J. F. Selection for male recombination in Drosophila melanogaster. Genetics 84, 333–351 (1976).

    CAS  PubMed  PubMed Central  Google Scholar 

  52. Rubin, G. M., Kidwell, M. G. & Bingham, P. M. The molecular basis of P-M hybrid dysgenesis: the nature of induced mutations. Cell 29, 987–994 (1982).

    CAS  PubMed  Google Scholar 

  53. Khurana, J. S. et al. Adaptation to P element transposon invasion in Drosophila melanogaster. Cell 147, 1551–1563 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Leitch, H. G., Tang, W. W. & Surani, M. A. Primordial germ-cell development and epigenetic reprogramming in mammals. Curr. Top. Dev. Biol. 104, 149–187 (2013).

    CAS  PubMed  Google Scholar 

  55. Chalvet, F. et al. Proviral amplification of the Gypsy endogenous retrovirus of Drosophila melanogaster involves env-independent invasion of the female germline. EMBO J. 18, 2659–2669 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Dewannieux, M. & Heidmann, T. L1-mediated retrotransposition of murine B1 and B2 SINEs recapitulated in cultured cells. J. Mol. Biol. 349, 241–247 (2005).

    CAS  PubMed  Google Scholar 

  57. Dewannieux, M., Dupressoir, A., Harper, F., Pierron, G. & Heidmann, T. Identification of autonomous IAP LTR retrotransposons mobile in mammalian cells. Nat. Genet. 36, 534–539 (2004).

    CAS  PubMed  Google Scholar 

  58. Davis, M. P. et al. Transposon-driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution. EMBO Rep. 18, 1231–1247 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Reuter, M. et al. Miwi catalysis is required for piRNA amplification-independent LINE1 transposon silencing. Nature 480, 264–267 (2011).

    CAS  PubMed  Google Scholar 

  60. Di Giacomo, M. et al. Multiple epigenetic mechanisms and the piRNA pathway enforce LINE1 silencing during adult spermatogenesis. Mol. Cell 50, 601–608 (2013).

    PubMed  Google Scholar 

  61. Klattenhoff, C. et al. The Drosophila HP1 homolog Rhino is required for transposon silencing and piRNA production by dual-strand clusters. Cell 138, 1137–1149 (2009). This study shows that the production of piRNA precursor transcripts from fly dual-strand clusters depends on the HP1 paralogue Rhino.

    CAS  PubMed  PubMed Central  Google Scholar 

  62. Mohn, F., Sienski, G., Handler, D. & Brennecke, J. The rhino-deadlock-cutoff complex licenses noncanonical transcription of dual-strand piRNA clusters in Drosophila. Cell 157, 1364–1379 (2014).

    CAS  PubMed  Google Scholar 

  63. Li, C. et al. Collapse of germline piRNAs in the absence of argonaute3 reveals somatic piRNAs in flies. Cell 137, 509–521 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  64. Malone, C. D. et al. Specialized piRNA pathways act in germline and somatic tissues of the Drosophila ovary. Cell 137, 522–535 (2009). References 63 and 64 report a specialized piRNA pathway in somatic follicle cells of fly ovaries.

    CAS  PubMed  PubMed Central  Google Scholar 

  65. Moshkovich, N. & Lei, E. P. HP1 recruitment in the absence of argonaute proteins in. Drosophila. PLOS Genet. 6, e1000880 (2010).

    PubMed  Google Scholar 

  66. Rangan, P. et al. piRNA production requires heterochromatin formation in Drosophila. Curr. Biol. 21, 1373–1379 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  67. Chen, Y. C. et al. Cutoff suppresses RNA polymerase II termination to ensure expression of piRNA precursors. Mol. Cell 63, 97–109 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  68. Pane, A., Jiang, P., Zhao, D. Y., Singh, M. & Schupbach, T. The Cutoff protein regulates piRNA cluster expression and piRNA production in the Drosophila germline. EMBO J. 30, 4601–4615 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  69. Andersen, P. R., Tirian, L., Vunjak, M. & Brennecke, J. A heterochromatin-dependent transcription machinery drives piRNA expression. Nature 549, 54–59 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Zhang, Z. et al. The HP1 homolog rhino anchors a nuclear complex that suppresses piRNA precursor splicing. Cell 157, 1353–1363 (2014). References 62, 69 and 70 collectively demonstrate that RNA Pol II transcription of piRNA precursor transcripts in fly dual-strand clusters is non-canonical: it is initiated on both genomic strands throughout the cluster and does not require promoter elements, and the transcription machinery ignores splicing and termination signals.

    CAS  PubMed  PubMed Central  Google Scholar 

  71. Hur, J. K. et al. Splicing-independent loading of TREX on nascent RNA is required for efficient expression of dual-strand piRNA clusters in Drosophila. Genes Dev. 30, 840–855 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Zhang, F. et al. UAP56 couples piRNA clusters to the perinuclear transposon silencing machinery. Cell 151, 871–884 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  73. Vermaak, D., Henikoff, S. & Malik, H. S. Positive selection drives the evolution of rhino, a member of the heterochromatin protein 1 family in Drosophila. PLOS Genet. 1, 96–108 (2005).

    CAS  PubMed  Google Scholar 

  74. Parhad, S. S., Tu, S., Weng, Z. & Theurkauf, W. E. Adaptive evolution leads to cross-species incompatibility in the piRNA transposon silencing machinery. Dev. Cell 43, 60–70 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  75. Mevel-Ninio, M., Pelisson, A., Kinder, J., Campos, A. R. & Bucheton, A. The flamenco locus controls the gypsy and ZAM retroviruses and is required for Drosophila oogenesis. Genetics 175, 1615–1624 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  76. Goriaux, C., Desset, S., Renaud, Y., Vaury, C. & Brasset, E. Transcriptional properties and splicing of the flamenco piRNA cluster. EMBO Rep. 15, 411–418 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  77. Zanni, V. et al. Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters. Proc. Natl Acad. Sci. USA 110, 19842–19847 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  78. Dennis, C., Brasset, E., Sarkar, A. & Vaury, C. Export of piRNA precursors by EJC triggers assembly of cytoplasmic Yb-body in Drosophila. Nat. Commun. 7, 13739 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  79. Handler, D. et al. The genetic makeup of the Drosophila piRNA pathway. Mol. Cell 50, 762–777 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  80. Muerdter, F. et al. A genome-wide RNAi screen draws a genetic framework for transposon control and primary piRNA biogenesis in Drosophila. Mol. Cell 50, 736–748 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  81. Ishizu, H. et al. Somatic primary piRNA biogenesis driven by cis-acting RNA elements and trans-acting Yb. 12, 429–440 Cell Rep. (2015).

    CAS  PubMed  Google Scholar 

  82. Homolka, D. et al. PIWI slicing and RNA elements in precursors instruct directional primary piRNA biogenesis. Cell Rep. 12, 418–428 (2015).

    CAS  PubMed  Google Scholar 

  83. Pandey, R. R. et al. Recruitment of Armitage and Yb to a transcript triggers its phased processing into primary piRNAs in Drosophila ovaries. PLOS Genet. 13, e1006956 (2017).

    PubMed  PubMed Central  Google Scholar 

  84. Molaro, A. et al. Two waves of de novo methylation during mouse germ cell development. Genes Dev. 28, 1544–1549 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  85. Gainetdinov, I., Colpan, C., Arif, A., Cecchini, K. & Zamore, P. D. A. Single mechanism of biogenesis, initiated and directed by PIWI proteins, explains piRNA production in most animals. Mol. Cell 71, 775–790 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  86. Robine, N. et al. A broadly conserved pathway generates 3ʹ UTR-directed primary piRNAs. Curr. Biol. 19, 2066–2076 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  87. Bolcun-Filas, E. et al. A-MYB (MYBL1) transcription factor is a master regulator of male meiosis. Development 138, 3319–3330 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  88. Weick, E. M. et al. PRDE-1 is a nuclear factor essential for the biogenesis of Ruby motif-dependent piRNAs in C. elegans. Genes Dev. 28, 783–796 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  89. Kasper, D. M., Wang, G., Gardner, K. E., Johnstone, T. G. & Reinke, V. The C. elegans SNAPc component SNPC-4 Coats piRNA domains and is globally required for piRNA abundance. Dev. Cell 31, 145–158 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  90. Beltran, T. et al. Evolutionary analysis implicates RNA polymerase II pausing and chromatin structure in nematode piRNA biogenesis. Preprint at bioRxiv https://www.biorxiv.org/content/early/2018/03/13/281360 (2018).

  91. Kawaoka, S., Izumi, N., Katsuma, S. & Tomari, Y. 3ʹ end formation of PIWI-interacting RNAs in vitro. Mol. Cell 43, 1015–1022 (2011).

    CAS  PubMed  Google Scholar 

  92. Cora, E. et al. The MID-PIWI module of Piwi proteins specifies nucleotide- and strand-biases of piRNAs. RNA 20, 773–781 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  93. Wang, W. et al. The initial uridine of primary piRNAs does not create the tenth adenine that is the hallmark of secondary piRNAs. Mol. Cell 56, 708–716 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  94. Matsumoto, N. et al. Crystal structure of silkworm PIWI-clade argonaute siwi bound to piRNA. Cell 167, 484–497 (2016).

    CAS  PubMed  Google Scholar 

  95. Mohn, F., Handler, D. & Brennecke, J. Noncoding, R. N. A. piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis. Science 348, 812–817 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  96. Han, B. W., Wang, W., Li, C., Weng, Z. & Zamore, P. D. Noncoding, R. N. A. piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production. Science 348, 817–821 (2015). References 82, 85, 95 and 96 collectively show that, in all animals, piRNA biogenesis is initiated by piRNA-guided PIWI cleavage and directed by PIWI proteins, yielding phased trailing pre-piRNAs.

    CAS  PubMed  PubMed Central  Google Scholar 

  97. Wang, W. et al. Slicing and binding by Ago3 or Aub trigger piwi-bound piRNA production by distinct mechanisms. Mol. Cell 59, 819–830 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  98. Gunawardane, L. S. et al. A slicer-mediated mechanism for repeat-associated siRNA 5ʹ end formation in Drosophila. Science 315, 1587–1590 (2007). References 20 and 98 discover the piRNA ping-pong pathway, the mechanism that amplifies piRNAs from a small population of maternally deposited or genomically encoded piRNAs.

    CAS  PubMed  Google Scholar 

  99. Haase, A. D. et al. Probing the initiation and effector phases of the somatic piRNA pathway in Drosophila. Genes Dev. 24, 2499–2504 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  100. Ipsaro, J. J., Haase, A. D., Knott, S. R., Joshua-Tor, L. & Hannon, G. J. The structural biochemistry of Zucchini implicates it as a nuclease in piRNA biogenesis. Nature 491, 279–283 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  101. Nishimasu, H. et al. Structure and function of Zucchini endoribonuclease in piRNA biogenesis. Nature 491, 284–287 (2012). References 94, 100 and 101 report the crystal structures of key endonucleases involved in piRNA biogenesis: fly Zucchini, mouse PLD6 and the silkmoth PIWI protein Siwi.

    CAS  PubMed  Google Scholar 

  102. Houwing, S., Berezikov, E. & Ketting, R. F. Zili is required for germ cell differentiation and meiosis in zebrafish. EMBO J. 27, 2702–2711 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  103. Haley, B. & Zamore, P. D. Kinetic analysis of the RNAi enzyme complex. Nat. Struct. Mol. Biol. 11, 599–606 (2004).

    CAS  PubMed  Google Scholar 

  104. Ma, J. B. et al. Structural basis for 5ʹ-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. Nature 434, 666–670 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  105. Parker, J. S., Roe, S. M. & Barford, D. Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex. Nature 434, 663–666 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  106. Wang, Y. et al. Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes. Nature 461, 754–761 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  107. Frank, F., Sonenberg, N. & Nagar, B. Structural basis for 5ʹ-nucleotide base-specific recognition of guide RNA by human AGO2. Nature 465, 818–822 (2010).

    CAS  PubMed  Google Scholar 

  108. Boland, A., Huntzinger, E., Schmidt, S., Izaurralde, E. & Weichenrieder, O. Crystal structure of the MID-PIWI lobe of a eukaryotic Argonaute protein. Proc. Natl Acad. Sci. USA 108, 10466–10471 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  109. Elkayam, E. et al. The structure of human Argonaute-2 in complex with miR-20a. Cell 150, 100–110 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  110. Schirle, N. T. & MacRae, I. J. The crystal structure of human Argonaute2. Science 336, 1037–1040 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  111. Schirle, N. T., Sheu-Gruttadauria, J. & MacRae, I. J. Structural basis for microRNA targeting. Science 346, 608–613 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  112. Matsumoto, N. et al. Crystal structure and activity of the endoribonuclease domain of the piRNA pathway factor maelstrom. Cell Rep. 11, 366–375 (2015).

    CAS  PubMed  Google Scholar 

  113. Lewis, B. P., Burge, C. B. & Bartel, D. P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120, 15–20 (2005).

    CAS  PubMed  Google Scholar 

  114. Grimson, A. et al. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell 27, 91–105 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  115. Nielsen, C. B. et al. Determinants of targeting by endogenous and exogenous microRNAs and siRNAs. RNA 13, 1894–1910 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  116. Baek, D. et al. The impact of microRNAs on protein output. Nature 455, 64–71 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  117. Selbach, M. et al. Widespread changes in protein synthesis induced by microRNAs. Nature 455, 58–63 (2008).

    CAS  PubMed  Google Scholar 

  118. Schirle, N. T., Sheu-Gruttadauria, J., Chandradoss, S. D., Joo, C. & MacRae, I. J. Water-mediated recognition of t1-adenosine anchors Argonaute2 to microRNA targets. eLife 4, e07646 (2015).

    PubMed Central  Google Scholar 

  119. Senti, K. A., Jurczak, D., Sachidanandam, R. & Brennecke, J. piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire. Genes Dev. 29, 1747–1762 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  120. Yang, Z. et al. PIWI slicing and EXD1 drive biogenesis of nuclear piRNAs from cytosolic targets of the mouse piRNA pathway. Mol. Cell 61, 138–152 (2016).

    PubMed  PubMed Central  Google Scholar 

  121. Tang, W., Tu, S., Lee, H. C., Weng, Z. & Mello, C. C. The RNase PARN-1 trims piRNA 3ʹ ends to promote transcriptome surveillance in C. elegans. Cell 164, 974–984 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  122. Izumi, N. et al. Identification and functional analysis of the pre-piRNA 3ʹ trimmer in silkworms. Cell 164, 962–973 (2016). References 91, 121 and 122 identify the exonuclease Trimmer (PNLDC1 in mice and PARN-1 in C. elegans ) as responsible for the final step of piRNA maturation, 3'-to-5' trimming.

    CAS  PubMed  PubMed Central  Google Scholar 

  123. Hayashi, R. et al. Genetic and mechanistic diversity of piRNA 3ʹ-end formation. Nature 539, 588–592 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  124. Ding, D. et al. PNLDC1 is essential for piRNA 3ʹ end trimming and transposon silencing during spermatogenesis in mice. Nat. Commun. 8, 819 (2017).

    PubMed  PubMed Central  Google Scholar 

  125. Zhang, Y. et al. An essential role for PNLDC1 in piRNA 3ʹ end trimming and male fertility in mice. Cell Res. 27, 1392–1396 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  126. Nishimura, T. et al. PNLDC1, mouse pre-piRNA Trimmer, is required for meiotic and post-meiotic male germ cell development. EMBO Rep. 19, e44957 (2018).

    PubMed  PubMed Central  Google Scholar 

  127. Hedges, S. B., Marin, J., Suleski, M., Paymer, M. & Kumar, S. Tree of life reveals clock-like speciation and diversification. Mol. Biol. Evol. 32, 835–845 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  128. Han, B. W., Hung, J. H., Weng, Z., Zamore, P. D. & Ameres, S. L. The 3ʹ-to-5ʹ exoribonuclease Nibbler shapes the 3ʹ ends of microRNAs bound to Drosophila Argonaute1. Curr. Biol. 21, 1878–1887 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  129. Liu, N. et al. The exoribonuclease Nibbler controls 3ʹ end processing of microRNAs in Drosophi la. Curr. Biol. 21, 1888–1893 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  130. Feltzin, V. L. et al. The exonuclease Nibbler regulates age-associated traits and modulates piRNA length in Drosophila. Aging Cell 14, 443–452 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  131. Li, J., Yang, Z., Yu, B., Liu, J. & Chen, X. Methylation protects miRNAs and siRNAs from a 3ʹ-end uridylation activity in Arabidopsis. Curr. Biol. 15, 1501–1507 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  132. Yu, B. et al. Methylation as a crucial step in plant microRNA biogenesis. Science 307, 932–935 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  133. Tian, Y., Simanshu, D. K., Ma, J. B. & Patel, D. J. Inaugural article: structural basis for piRNA 2ʹ-O-methylated 3ʹ-end recognition by Piwi PAZ (Piwi/Argonaute/Zwille) domains. Proc. Natl Acad. Sci. USA 108, 903–910 (2011).

    CAS  PubMed  Google Scholar 

  134. Simon, B. et al. Recognition of 2ʹ-O-methylated 3ʹ-end of piRNA by the PAZ domain of a piwi protein. Structure 19, 172–180 (2011).

    CAS  PubMed  Google Scholar 

  135. Zeng, L., Zhang, Q., Yan, K. & Zhou, M. M. Structural insights into piRNA recognition by the human PIWI-like 1 PAZ domain. Proteins 79, 2004–2009 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  136. Liang, L., Diehl-Jones, W. & Lasko, P. Localization of vasa protein to the Drosophila pole plasm is independent of its RNA-binding and helicase activities. Development 120, 1201–1211 (1994).

    CAS  PubMed  Google Scholar 

  137. Harris, A. N. & Macdonald, P. M. aubergine encodes a Drosophila polar granule component required for pole cell formation and related to eIF2C. Development 128, 2823–2832 (2001).

    CAS  PubMed  Google Scholar 

  138. Findley, S. D., Tamanaha, M., Clegg, N. J. & Ruohola-Baker, H. Maelstrom, a Drosophila spindle-class gene, encodes a protein that colocalizes with Vasa and RDE1/AGO1 homolog, Aubergine, in nuage. Development 130, 859–871 (2003).

    CAS  PubMed  Google Scholar 

  139. Lim, A. K. & Kai, T. Unique germ-line organelle, nuage, functions to repress selfish genetic elements in Drosophila melanogaster. Proc. Natl Acad. Sci. USA 104, 6714–6719 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  140. Zhang, Z. et al. Heterotypic piRNA ping-pong requires Qin, a protein with both E3-ligase and tudor domains. Mol. Cell 44, 572–584 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  141. Chuma, S. et al. Tdrd1/Mtr-1, a tudor-related gene, is essential for male germ-cell differentiation and nuage/germinal granule formation in mice. Proc. Natl Acad. Sci. USA 103, 15894–15899 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  142. Aravin, A. A. et al. Cytoplasmic compartmentalization of the fetal piRNA pathway in mice. PLOS Genet. 5, e1000764 (2009).

    PubMed  PubMed Central  Google Scholar 

  143. Eddy, E. M. Germ plasm and the differentiation of the germ cell line. Int. Rev. Cytol. 43, 229–280 (1975).

    CAS  PubMed  Google Scholar 

  144. Shoji, M. et al. The TDRD9-MIWI2 complex is essential for piRNA-mediated retrotransposon silencing in the mouse male germline. Dev. Cell 17, 775–787 (2009).

    CAS  PubMed  Google Scholar 

  145. Choi, S. Y. et al. A common lipid links Mfn-mediated mitochondrial fusion and SNARE-regulated exocytosis. Nat. Cell Biol. 8, 1255–1262 (2006).

    CAS  PubMed  Google Scholar 

  146. Wang, S. et al. Cloning and functional characterization of a novel mitochondrial N-ethylmaleimide-sensitive glycerol-3-phosphate acyltransferase (GPAT2). Arch. Biochem. Biophys. 465, 347–358 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  147. Saito, K. et al. Roles for the Yb body components Armitage and Yb in primary piRNA biogenesis in Drosophila. Genes Dev. 24, 2493–2498 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  148. Watanabe, T. et al. MITOPLD is a mitochondrial protein essential for nuage formation and piRNA biogenesis in the mouse germline. Dev. Cell 20, 364–375 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  149. Huang, H. et al. piRNA-associated germline nuage formation and spermatogenesis require MitoPLD profusogenic mitochondrial-surface lipid signaling. Dev. Cell 20, 376–387 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  150. Honda, S. et al. Mitochondrial protein BmPAPI modulates the length of mature piRNAs. RNA 19, 1405–1418 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  151. Saxe, J. P., Chen, M., Zhao, H. & Lin, H. Tdrkh is essential for spermatogenesis and participates in primary piRNA biogenesis in the germline. EMBO J. 32, 1869–1885 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  152. Szakmary, A., Reedy, M., Qi, H. & Lin, H. The Yb protein defines a novel organelle and regulates male germline stem cell self-renewal in Drosophila melanogaster. J. Cell Biol. 185, 613–627 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  153. Eddy, E. M. Fine structural observations on the form and distribution of nuage in germ cells of the rat. Anat. Rec. 178, 731–757 (1974).

    CAS  PubMed  Google Scholar 

  154. Rogers, A. K., Situ, K., Perkins, E. M. & Toth, K. F. Zucchini-dependent piRNA processing is triggered by recruitment to the cytoplasmic processing machinery. Genes Dev. 31, 1858–1869 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  155. Siomi, M. C., Mannen, T. & Siomi, H. How does the royal family of Tudor rule the PIWI-interacting RNA pathway? Genes Dev. 24, 636–646 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  156. Chen, C. et al. Mouse Piwi interactome identifies binding mechanism of Tdrkh Tudor domain to arginine methylated Miwi. Proc. Natl Acad. Sci. USA 106, 20336–20341 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  157. Nishida, K. M. et al. Functional involvement of Tudor and dPRMT5 in the piRNA processing pathway in Drosophila germlines. EMBO J. 28, 3820–3831 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  158. Reuter, M. et al. Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA profile. Nat. Struct. Mol. Biol. 16, 639–646 (2009).

    CAS  PubMed  Google Scholar 

  159. Wang, J., Saxe, J. P., Tanaka, T., Chuma, S. & Lin, H. Mili interacts with Tudor domain-containing protein 1 in regulating spermatogenesis. Curr. Biol. 19, 640–644 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  160. Vagin, V. V. et al. Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members. Genes Dev. 23, 1749–1762 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  161. Kirino, Y. et al. Arginine methylation of vasa protein is conserved across phyla. J. Biol. Chem. 285, 8148–8154 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  162. Huang, H. Y. et al. Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. EMBO J. 30, 3298–3308 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  163. Patil, V. S. & Kai, T. Repression of retroelements in Drosophila germline via piRNA pathway by the tudor domain protein Tejas. Curr. Biol. 20, 724–730 (2010).

    CAS  PubMed  Google Scholar 

  164. Anand, A. & Kai, T. The tudor domain protein Kumo is required to assemble the nuage and to generate germline piRNAs in Drosophila. EMBO J. 31, 870–882 (2012).

    CAS  PubMed  Google Scholar 

  165. Webster, A. et al. Aub and Ago3 are recruited to nuage through two mechanisms to form a ping-pong complex assembled by Krimper. Mol. Cell 59, 564–575 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  166. Sato, K. et al. Krimper enforces an antisense bias on piRNA pools by binding AGO3 in the Drosophila germline. Mol. Cell 59, 553–563 (2015).

    CAS  PubMed  Google Scholar 

  167. Nishida, K. M. et al. Hierarchical roles of mitochondrial Papi and Zucchini in Bombyx germline piRNA biogenesis. Nature 555, 260–264 (2018).

    CAS  PubMed  Google Scholar 

  168. De Fazio, S. et al. The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements. Nature 480, 259–263 (2011). References 59 and 168 report that mammalian cytoplasmic PIWI proteins repress transposons by cleaving their mRNAs.

    PubMed  Google Scholar 

  169. Juliano, C. E. et al. PIWI proteins and PIWI-interacting RNAs function in Hydra somatic stem cells. Proc. Natl Acad. Sci. USA 111, 337–342 (2014).

    CAS  PubMed  Google Scholar 

  170. Roovers, E. F. et al. Piwi proteins and piRNAs in mammalian oocytes and early embryos. Cell Rep. 10, 2069–2082 (2015).

    CAS  PubMed  Google Scholar 

  171. Praher, D. et al. Characterization of the piRNA pathway during development of the sea anemone Nematostella vectensis. RNA Biol. 14, 1727–1741 (2017).

    PubMed  PubMed Central  Google Scholar 

  172. Gainetdinov, I., Skvortsova, Y., Kondratieva, S., Funikov, S. & Azhikina, T. Two modes of targeting transposable elements by piRNA pathway in human testis. RNA 23, 1614–1625 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  173. Morazzani, E. M., Wiley, M. R., Murreddu, M. G., Adelman, Z. N. & Myles, K. M. Production of virus-derived ping-pong-dependent piRNA-like small RNAs in the mosquito soma. PLOS Pathog. 8, e1002470 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  174. Schnettler, E. et al. Knockdown of piRNA pathway proteins results in enhanced Semliki Forest virus production in mosquito cells. J. Gen. Virol. 94, 1680–1689 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  175. Miesen, P., Girardi, E. & van Rij, R. P. Distinct sets of PIWI proteins produce arbovirus and transposon-derived piRNAs in Aedes aegypti mosquito cells. Nucleic Acids Res. 43, 6545–6556 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  176. Goodier, J. L. & Kazazian, H. H. Retrotransposons revisited: the restraint and rehabilitation of parasites. Cell 135, 23–35 (2008).

    CAS  PubMed  Google Scholar 

  177. Zamudio, N. et al. DNA methylation restrains transposons from adopting a chromatin signature permissive for meiotic recombination. Genes Dev. 29, 1256–1270 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  178. Vasiliauskaite˙, L. et al. Defective germline reprogramming rewires the spermatogonial transcriptome. Nat. Struct. Mol. Biol. 25, 394–404 (2018).

    PubMed  PubMed Central  Google Scholar 

  179. Jehn, J. et al. PIWI genes and piRNAs are ubiquitously expressed in mollusks and show patterns of lineage-specific adaptation. Commun. Biol. 1, 137 (2018).

    PubMed  PubMed Central  Google Scholar 

  180. Savitsky, M., Kwon, D., Georgiev, P., Kalmykova, A. & Gvozdev, V. Telomere elongation is under the control of the RNAi-based mechanism in the Drosophila germline. Genes Dev. 20, 345–354 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  181. Khurana, J. S., Xu, J., Weng, Z. & Theurkauf, W. E. Distinct functions for the Drosophila piRNA pathway in genome maintenance and telomere protection. PLOS Genet. 6, e1001246 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  182. Radion, E. et al. Key role of piRNAs in telomeric chromatin maintenance and telomere nuclear positioning in Drosophila germline. Epigenetics Chromatin 11, 40 (2018).

    PubMed  PubMed Central  Google Scholar 

  183. Pardue, M. L. & DeBaryshe, P. G. Drosophila telomeres: a variation on the telomerase theme. Fly (Austin) 2, 101–110 (2008).

    Google Scholar 

  184. Pardue, M. L. & Debaryshe, P. Adapting to life at the end of the line: how Drosophila telomeric retrotransposons cope with their job. Mob. Genet. Elements 1, 128–134 (2011).

    PubMed  PubMed Central  Google Scholar 

  185. Klenov, M. S. et al. Repeat-associated siRNAs cause chromatin silencing of retrotransposons in the Drosophila melanogaster germline. Nucleic Acids Res. 35, 5430–5438 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  186. Wang, S. H. & Elgin, S. C. Drosophila Piwi functions downstream of piRNA production mediating a chromatin-based transposon silencing mechanism in female germ line. Proc. Natl Acad. Sci. USA 108, 21164–21169 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  187. Klenov, M. S. et al. Separation of stem cell maintenance and transposon silencing functions of Piwi protein. Proc. Natl Acad. Sci. USA 108, 18760–18765 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  188. Sienski, G., Donertas, D. & Brennecke, J. Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression. Cell 151, 964–980 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  189. Le Thomas, A. et al. Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state. Genes Dev. 27, 390–399 (2013).

    PubMed  PubMed Central  Google Scholar 

  190. Rozhkov, N. V., Hammell, M. & Hannon, G. J. Multiple roles for Piwi in silencing Drosophila transposons. Genes Dev. 27, 400–412 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  191. Verdel, A. et al. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303, 672–676 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  192. Darricarrère, N., Liu, N., Watanabe, T. & Lin, H. Function of Piwi, a nuclear Piwi/Argonaute protein, is independent of its slicer activity. Proc. Natl Acad. Sci. USA 110, 1297–1302 (2013). References 168 and 192 demonstrate that piRNA-guided transcriptional repression does not require nuclear PIWI slicer activity.

    PubMed  PubMed Central  Google Scholar 

  193. Sienski, G. et al. Silencio/CG9754 connects the Piwi-piRNA complex to the cellular heterochromatin machinery. Genes Dev. 29, 2258–2271 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  194. Yu, Y. et al. Panoramix enforces piRNA-dependent cotranscriptional silencing. Science 350, 339–342 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  195. Ohtani, H. et al. DmGTSF1 is necessary for Piwi-piRISC-mediated transcriptional transposon silencing in the Drosophila ovary. Genes Dev. 27, 1656–1661 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  196. Iwasaki, Y. W. et al. Piwi modulates chromatin accessibility by regulating multiple factors including histone H1 to repress transposons. Mol. Cell 63, 408–419 (2016).

    CAS  PubMed  Google Scholar 

  197. Teixeira, F. K. et al. piRNA-mediated regulation of transposon alternative splicing in the soma and germ line. Nature 552, 268–272 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  198. Shpiz, S., Ryazansky, S., Olovnikov, I., Abramov, Y. & Kalmykova, A. Euchromatic transposon insertions trigger production of novel Pi and endo-siRNAs at the target sites in the drosophila germline. PLOS Genet. 10, e1004138 (2014).

    PubMed  PubMed Central  Google Scholar 

  199. Carmell, M. A. et al. MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Dev. Cell 12, 503–514 (2007).

    CAS  PubMed  Google Scholar 

  200. Aravin, A. A., Hannon, G. J. & Brennecke, J. The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science 318, 761–764 (2007).

    CAS  PubMed  Google Scholar 

  201. Pezic, D., Manakov, S. A., Sachidanandam, R. & Aravin, A. A. piRNA pathway targets active LINE1 elements to establish the repressive H3K9me3 mark in germ cells. Genes Dev. 28, 1410–1428 (2014). References 188 and 201 provide genome-wide evidence that piRNAs silence transposons transcriptionally by directing repressive chromatin marks.

    CAS  PubMed  PubMed Central  Google Scholar 

  202. Manakov, S. A. et al. MIWI2 and MILI have differential effects on piRNA biogenesis and DNA methylation. Cell Rep. 12, 1234–1243 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  203. Nagamori, I. et al. Comprehensive DNA methylation analysis of retrotransposons in male germ cells. Cell Rep. 12, 1541–1547 (2015).

    CAS  PubMed  Google Scholar 

  204. Kojima-Kita, K. et al. MIWI2 as an effector of DNA methylation and gene silencing in embryonic male germ cells. Cell Rep. 16, 2819–2828 (2016).

    CAS  PubMed  Google Scholar 

  205. Vasiliauskaite˙, L. et al. A MILI-independent piRNA biogenesis pathway empowers partial germline reprogramming. Nat. Struct. Mol. Biol. 24, 604–606 (2017).

    PubMed  Google Scholar 

  206. Barau, J. et al. The DNA methyltransferase DNMT3C protects male germ cells from transposon activity. Science 354, 909–912 (2016).

    CAS  PubMed  Google Scholar 

  207. Jain, D. et al. rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline. PLOS Genet. 13, e1006964 (2017).

    PubMed  PubMed Central  Google Scholar 

  208. Di Giacomo, M., Comazzetto, S., Sampath, S. C., Sampath, S. C. & O’Carroll, D. G9a co-suppresses LINE1 elements in spermatogonia. Epigenetics Chromatin 7, 24 (2014).

    PubMed  PubMed Central  Google Scholar 

  209. Grentzinger, T. et al. piRNA-mediated transgenerational inheritance of an acquired trait. Genome Res. 22, 1877–1888 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  210. Lee, H. C. et al. C. elegans piRNAs mediate the genome-wide surveillance of germline transcripts. Cell 150, 78–87 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  211. Bagijn, M. P. et al. Function, targets, and evolution of Caenorhabditis elegans piRNAs. Science 337, 574–578 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  212. Shen, E. Z. et al. Identification of piRNA binding sites reveals the argonaute regulatory landscape of the C. elegans Germline. Cell 172, 937–951 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  213. Zhang, D. et al. The piRNA targeting rules and the resistance to piRNA silencing in endogenous genes. Science 359, 587–592 (2018). References 212 and 213 demonstrate that C. elegans piRNAs target virtually all germline transcripts through miRNA-like pairing rules.

    CAS  PubMed  PubMed Central  Google Scholar 

  214. Claycomb, J. M. et al. The Argonaute CSR-1 and its 22G-RNA cofactors are required for holocentric chromosome segregation. Cell 139, 123–134 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  215. Shirayama, M. et al. piRNAs initiate an epigenetic memory of nonself RNA in the C. elegans germline. Cell 150, 65–77 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  216. Wedeles, C. J., Wu, M. Z. & Claycomb, J. M. Protection of germline gene expression by the C. elegans Argonaute CSR-1. Dev. Cell 27, 664–671 (2013).

    CAS  PubMed  Google Scholar 

  217. Seth, M. et al. The C. elegans CSR-1 argonaute pathway counteracts epigenetic silencing to promote germline gene expression. Dev. Cell 27, 656–663 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  218. Ashe, A. et al. piRNAs can trigger a multigenerational epigenetic memory in the germline of C. elegans. Cell 150, 88–99 (2012).

    CAS  PubMed  Google Scholar 

  219. Luteijn, M. J. et al. Extremely stable Piwi-induced gene silencing in Caenorhabditis elegans. EMBO J. 31, 3422–3430 (2012). References 210, 211, 215, 218 and 219 reveal that the worm PIWI protein PRG-1 initiates a secondary siRNA response to silence its targets.

    CAS  PubMed  PubMed Central  Google Scholar 

  220. Buckley, B. A. et al. A nuclear Argonaute promotes multigenerational epigenetic inheritance and germline immortality. Nature 489, 447–451 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  221. de Albuquerque, B. F., Placentino, M. & Ketting, R. F. Maternal piRNAs are essential for germline development following de novo establishment of endo-siRNAs in Caenorhabditis elegans. Dev. Cell 34, 448–456 (2015).

    PubMed  Google Scholar 

  222. Palatini, U. et al. Comparative genomics shows that viral integrations are abundant and express piRNAs in the arboviral vectors Aedes aegypti and Aedes albopictus. BMC Genomics 18, 512 (2017).

    PubMed  PubMed Central  Google Scholar 

  223. Whitfield, Z. J. et al. The diversity, structure, and function of heritable adaptive immunity sequences in the Aedes aegypti genome. Curr. Biol. 27, 3511–3519 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  224. Wu, P.-H. et al. An evolutionarily conserved piRNA-producing locus required for male mouse fertility. Preprint at bioRxiv https://www.biorxiv.org/content/early/2018/08/07/386201 (2018).

  225. Gou, L. T. et al. Pachytene piRNAs instruct massive mRNA elimination during late spermiogenesis. Cell Res. 24, 680–700 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  226. Vourekas, A. et al. Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis. Nat. Struct. Mol. Biol. 19, 773–781 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  227. Goh, W. S. et al. piRNA-directed cleavage of meiotic transcripts regulates spermatogenesis. Genes Dev. 29, 1032–1044 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  228. Zhang, P. et al. MIWI and piRNA-mediated cleavage of messenger RNAs in mouse testes. Cell Res. 25, 193–207 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  229. Lin, H. & Spradling, A. C. A novel group of pumilio mutations affects the asymmetric division of germline stem cells in the Drosophila ovary. Development 124, 2463–2476 (1997).

    CAS  PubMed  Google Scholar 

  230. Cox, D. N. et al. A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell self-renewal. Genes Dev. 12, 3715–3727 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  231. Juliano, C., Wang, J. & Lin, H. Uniting germline and stem cells: the function of Piwi proteins and the piRNA pathway in diverse organisms. Annu. Rev. Genet. 45, 447–469 (2011).

    CAS  PubMed  Google Scholar 

  232. Rouget, C. et al. Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo. Nature 467, 1128–1132 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  233. Barckmann, B. et al. Aubergine iCLIP reveals piRNA-dependent decay of mRNAs involved in germ cell development in the early embryo. Cell Rep. 12, 1205–1216 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  234. Gavis, E. R., Lunsford, L., Bergsten, S. E. & Lehmann, R. A conserved 90 nucleotide element mediates translational repression of nanos RNA. Development 122, 2791–2800 (1996).

    CAS  PubMed  Google Scholar 

  235. Gavis, E. R., Curtis, D. & Lehmann, R. Identification of cis-acting sequences that control nanos RNA localization. Dev. Biol. 176, 36–50 (1996).

    CAS  PubMed  Google Scholar 

  236. Handler, D. et al. A systematic analysis of Drosophila TUDOR domain-containing proteins identifies Vreteno and the Tdrd12 family as essential primary piRNA pathway factors. EMBO J. 30, 3977–3993 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  237. Simkin, A., Wong, A., Poh, Y.-P., Theurkauf, W. E. & Jensen, J. D. Recurrent and recent selective sweeps in the piRNA pathway. Evolution 67, 1081–1090 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  238. Palmer, W. H., Hadfield, J. D. & Obbard, D. J. RNA-interference pathways display high rates of adaptive protein evolution in multiple invertebrates. Genetics 208, 1585–1599 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  239. Cenik, E. S. & Zamore, P. D. Argonaute proteins. Curr. Biol. 21, R446–R449 (2011).

    CAS  PubMed  Google Scholar 

  240. Czech, B. & Hannon, G. J. Small RNA sorting: matchmaking for Argonautes. Nat. Rev. Genet. 12, 19–31 (2011).

    CAS  PubMed  Google Scholar 

  241. Hammond, S. M., Boettcher, S., Caudy, A. A., Kobayashi, R. & Hannon, G. J. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293, 1146–1150 (2001).

    CAS  PubMed  Google Scholar 

  242. Martinez, J., Patkaniowska, A., Urlaub, H., Lührmann, R. & Tuschl, T. Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 110, 563–574 (2002).

    CAS  PubMed  Google Scholar 

  243. Nykanen, A., Haley, B. & Zamore, P. D. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107, 309–321 (2001).

    CAS  PubMed  Google Scholar 

  244. Hutvágner, G. et al. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293, 834–838 (2001).

    PubMed  Google Scholar 

  245. Mourelatos, Z. et al. miRNPs: a novel class of Ribonucleoproteins containing numerous microRNAs. Genes Dev. 16, 720–728 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  246. Tabara, H. et al. The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell 99, 123–132 (1999).

    CAS  PubMed  Google Scholar 

  247. Lee, Y. et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 425, 415–419 (2003).

    CAS  PubMed  Google Scholar 

  248. Bernstein, E., Caudy, A. A., Hammond, S. M. & Hannon, G. J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409, 363–366 (2001).

    CAS  PubMed  Google Scholar 

  249. Grishok, A. et al. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106, 23–34 (2001).

    CAS  PubMed  Google Scholar 

  250. Knight, S. W. & Bass, B. L. A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 293, 2269–2271 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  251. Schwarz, D. S. et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199–208 (2003).

    CAS  PubMed  Google Scholar 

  252. Khvorova, A., Reynolds, A. & Jayasena, S. D. Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209–216 (2003).

    CAS  PubMed  Google Scholar 

  253. Aza-Blanc, P. et al. Identification of modulators of TRAIL-induced apoptosis via RNAi-based phenotypic screening. Mol. Cell 12, 627–637 (2003).

    CAS  PubMed  Google Scholar 

  254. Tomari, Y., Matranga, C., Haley, B., Martinez, N. & Zamore, P. D. A protein sensor for siRNA asymmetry. Science 306, 1377–1380 (2004).

    CAS  PubMed  Google Scholar 

  255. Ghildiyal, M., Xu, J., Seitz, H., Weng, Z. & Zamore, P. D. Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. RNA 16, 43–56 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  256. Kim, K., Lee, Y. S. & Carthew, R. W. Conversion of pre-RISC to holo-RISC by Ago2 during assembly of RNAi complexes. RNA 13, 22–29 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  257. Leuschner, P. J., Ameres, S. L., Kueng, S. & Martinez, J. Cleavage of the siRNA passenger strand during RISC assembly in human cells. EMBO Rep. 7, 314–320 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  258. Matranga, C., Tomari, Y., Shin, C., Bartel, D. P. & Zamore, P. D. Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. Cell 123, 607–620 (2005).

    CAS  PubMed  Google Scholar 

  259. Pelisson, A., Sarot, E., Payen-Groschene, G. & Bucheton, A. A novel repeat-associated small interfering RNA-mediated silencing pathway downregulates complementary sense gypsy transcripts in somatic cells of the Drosophila ovary. J. Virol. 81, 1951–1960 (2007).

    CAS  PubMed  Google Scholar 

  260. Kirino, Y. & Mourelatos, Z. 2ʹ-O-methyl modification in mouse piRNAs and its methylase. Nucleic Acids Symp. Ser. (Oxf.) 51, 417–418 (2007).

    Google Scholar 

  261. Lingel, A., Simon, B., Izaurralde, E. & Sattler, M. Nucleic acid 3ʹ-end recognition by the Argonaute2 PAZ domain. Nat. Struct. Mol. Biol. 11, 576–577 (2004).

    CAS  PubMed  Google Scholar 

  262. Song, J. J. et al. The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat. Struct. Biol. 10, 1026–1032 (2003).

    CAS  PubMed  Google Scholar 

  263. Ma, J. B., Ye, K. & Patel, D. J. Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature 429, 318–322 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  264. Parker, J. S., Parizotto, E. A., Wang, M., Roe, S. M. & Barford, D. Enhancement of the seed-target recognition step in RNA silencing by a PIWI/MID domain protein. Mol. Cell 33, 204–214 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  265. Elbashir, S. M., Martinez, J., Patkaniowska, A., Lendeckel, W. & Tuschl, T. Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J. 20, 6877–6888 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  266. Elbashir, S. M., Lendeckel, W. & Tuschl, T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev. 15, 188–200 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  267. Parker, J. S., Roe, S. M. & Barford, D. Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO J. 23, 4727–4737 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  268. Schwarz, D. S., Tomari, Y. & Zamore, P. D. The RNA-induced silencing complex Is a Mg2+-dependent endonuclease. Curr. Biol. 14, 787–791 (2004).

    CAS  PubMed  Google Scholar 

  269. Yuan, Y. R. et al. Crystal structure of A. aeolicus Argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage. Mol. Cell 19, 405–419 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  270. German, M. A. et al. Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat. Biotechnol. 26, 941–946 (2008).

    CAS  PubMed  Google Scholar 

  271. Addo-Quaye, C., Eshoo, T. W., Bartel, D. P. & Axtell, M. J. Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Curr. Biol. 18, 758–762 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  272. Addo-Quaye, C. et al. Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome. RNA 15, 2112–2121 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  273. German, M. A., Luo, S., Schroth, G., Meyers, B. C. & Green, P. J. Construction of parallel analysis of RNA ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome. Nat. Protoc. 4, 356–362 (2009).

    CAS  PubMed  Google Scholar 

  274. Fawcett, D. W., Eddy, E. M. & Phillips, D. M. Observations on the fine structure and relationships of the chromatoid body in mammalian spermatogenesis. Biol. Reprod. 2, 129–153 (1970).

    CAS  PubMed  Google Scholar 

  275. Benda, C. Neue mitteilungen über die entwicklung der genitredrüsen und über die metamorphose der samenzellen [German]. Arch. Anat. Physiol. 549–552 (1891).

  276. Mahowald, A. Polar granules of Drosophila. III. The continuity of polar granules during the life cycle of Drosophila. J. Exp. Zool. 176, 329–343 (1971).

    CAS  PubMed  Google Scholar 

  277. Braat, A. K., Zandbergen, T., van de Water, S., Goos, H. J. & Zivkovic, D. Characterization of zebrafish primordial germ cells: morphology and early distribution of vasa RNA. Dev. Dyn. 216, 153–167 (1999).

    CAS  PubMed  Google Scholar 

  278. Strome, S. & Wood, W. B. Immunofluorescence visualization of germ-line-specific cytoplasmic granules in embryos, larvae, and adults of Caenorhabditis elegans. Proc. Natl Acad. Sci. USA 79, 1558–1562 (1982).

    CAS  PubMed  PubMed Central  Google Scholar 

  279. Wolf, N., Priess, J. & Hirsh, D. Segregation of germline granules in early embryos of Caenorhabditis elegans: an electron microscopic analysis. J. Embryol. Exp. Morphol. 73, 297–306 (1983).

    CAS  PubMed  Google Scholar 

  280. Updike, D. & Strome, S. P granule assembly and function in Caenorhabditis elegans germ cells. J. Androl. 31, 53–60 (2010).

    CAS  PubMed  Google Scholar 

  281. Hanazawa, M., Yonetani, M. & Sugimoto, A. PGL proteins self associate and bind RNPs to mediate germ granule assembly in C. elegans. J. Cell Biol. 192, 929–937 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  282. Olivieri, D., Sykora, M. M., Sachidanandam, R., Mechtler, K. & Brennecke, J. An in vivo RNAi assay identifies major genetic and cellular requirements for primary piRNA biogenesis in Drosophila. EMBO J. 29, 3301–3317 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  283. Banani, S. F., Lee, H. O., Hyman, A. A. & Rosen, M. K. Biomolecular condensates: organizers of cellular biochemistry. Nat. Rev. Mol. Cell Biol. 18, 285–298 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  284. Seydoux, G. The P granules of C. elegans: a genetic model for the study of RNA-protein condensates. J. Mol. Biol. https://doi.org/10.1016/j.jmb.2018.08.007 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  285. Brangwynne, C. P. et al. Germline P granules are liquid droplets that localize by controlled dissolution/condensation. Science 324, 1729–1732 (2009).

    CAS  PubMed  Google Scholar 

  286. Nott, T. J. et al. Phase transition of a disordered nuage protein generates environmentally responsive membraneless organelles. Mol. Cell 57, 936–947 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  287. Chen, C., Nott, T. J., Jin, J. & Pawson, T. Deciphering arginine methylation: Tudor tells the tale. Nat. Rev. Mol. Cell Biol. 12, 629–642 (2011).

    CAS  PubMed  Google Scholar 

  288. Cox, D. N., Chao, A. & Lin, H. piwi encodes a nucleoplasmic factor whose activity modulates the number and division rate of germline stem cells. Development 127, 503–514 (2000).

    CAS  PubMed  Google Scholar 

  289. Dönertas, D., Sienski, G. & Brennecke, J. Drosophila Gtsf1 is an essential component of the Piwi-mediated transcriptional silencing complex. Genes Dev. 27, 1693–1705 (2013).

    PubMed  PubMed Central  Google Scholar 

  290. Yoshimura, T. et al. Gtsf1/Cue110, a gene encoding a protein with two copies of a CHHC Zn-finger motif, is involved in spermatogenesis and retrotransposon suppression in murine testes. Dev. Biol. 335, 216–227 (2009).

    CAS  PubMed  Google Scholar 

  291. Yoshimura, T. et al. Mouse GTSF1 is an essential factor for secondary piRNA biogenesis. EMBO Rep. 19, e42054 (2018).

    PubMed  PubMed Central  Google Scholar 

  292. Soper, S. F. et al. Mouse maelstrom, a component of nuage, is essential for spermatogenesis and transposon repression in meiosis. Dev. Cell 15, 285–297 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  293. Castaneda, J. et al. Reduced pachytene piRNAs and translation underlie spermiogenic arrest in Maelstrom mutant mice. EMBO J. 33, 1999–2019 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  294. Schupbach, T. & Wieschaus, E. Female sterile mutations on the second chromosome of Drosophila melanogaster. II. Mutations blocking oogenesis or altering egg morphology. Genetics 129, 1119–1136 (1991).

    CAS  PubMed  PubMed Central  Google Scholar 

  295. Kuramochi-Miyagawa, S. et al. Two mouse piwi-related genes: miwi and mili. Mech. Dev. 108, 121–133 (2001).

    CAS  PubMed  Google Scholar 

  296. Deng, W. & Lin, H. miwi, a murine homolog of piwi, encodes a cytoplasmic protein essential for spermatogenesis. Dev. Cell 2, 819–830 (2002).

    CAS  PubMed  Google Scholar 

  297. Kuramochi-Miyagawa, S. et al. Mili, a mammalian member of piwi family gene, is essential for spermatogenesis. Development 131, 839–849 (2004).

    CAS  PubMed  Google Scholar 

  298. Klattenhoff, C. et al. Drosophila rasiRNA pathway mutations disrupt embryonic axis specification through activation of an ATR/Chk2 DNA damage response. Dev. Cell 12, 45–55 (2007). This study demonstrates that the fly genes armitage and aubergine do not regulate embryonic axis specification but are components of the piRNA pathway.

    CAS  PubMed  Google Scholar 

  299. Huang, H. et al. AGO3 Slicer activity regulates mitochondria-nuage localization of Armitage and piRNA amplification. J. Cell Biol. 206, 217–230 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  300. Pane, A., Wehr, K. & Schupbach, T. zucchini and squash encode two putative nucleases required for rasiRNA production in the Drosophila germline. Dev. Cell 12, 851–862 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  301. Vagin, V. V. et al. Minotaur is critical for primary piRNA biogenesis. RNA 19, 1064–1077 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  302. Shiromoto, Y. et al. GPAT2, a mitochondrial outer membrane protein, in piRNA biogenesis in germline stem cells. RNA 19, 803–810 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  303. Ma, L. et al. GASZ is essential for male meiosis and suppression of retrotransposon expression in the male germline. PLOS Genet. 5, e1000635 (2009).

    PubMed  PubMed Central  Google Scholar 

  304. Czech, B., Preall, J. B., McGinn, J. & Hannon, G. J. A transcriptome-wide RNAi screen in the Drosophila ovary reveals factors of the germline piRNA pathway. Mol. Cell 50, 749–761 (2013). References 79, 80 and 304 use genetic screens in flies to identify an extensive set of piRNA pathway components.

    CAS  PubMed  PubMed Central  Google Scholar 

  305. Cook, H. A., Koppetsch, B. S., Wu, J. & Theurkauf, W. E. The Drosophila SDE3 homolog armitage is required for oskar mRNA silencing and embryonic axis specification. Cell 116, 817–829 (2004).

    CAS  PubMed  Google Scholar 

  306. Zheng, K. et al. Mouse MOV10L1 associates with Piwi proteins and is an essential component of the Piwi-interacting RNA (piRNA) pathway. Proc. Natl Acad. Sci. USA 107, 11841–11846 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  307. Frost, R. J. et al. MOV10L1 is necessary for protection of spermatocytes against retrotransposons by Piwi-interacting RNAs. Proc. Natl Acad. Sci. USA 107, 11847–11852 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  308. Zheng, K. & Wang, P. J. Blockade of pachytene piRNA biogenesis reveals a novel requirement for maintaining post-meiotic germline genome integrity. PLOS Genet. 8, e1003038 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  309. Vourekas, A. et al. The RNA helicase MOV10L1 binds piRNA precursors to initiate piRNA processing. Genes Dev. 29, 617–629 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  310. Fu, Q., Pandey, R. R., Leu, N. A., Pillai, R. S. & Wang, P. J. Mutations in the MOV10L1 ATP hydrolysis motif cause piRNA biogenesis failure and male sterility in mice. Biol. Reprod. 95, 103 (2016).

    PubMed  PubMed Central  Google Scholar 

  311. Xiol, J. et al. RNA clamping by vasa assembles a piRNA amplifier complex on transposon transcripts. Cell 157, 1698–1711 (2014).

    CAS  PubMed  Google Scholar 

  312. Nishida, K. M. et al. Respective functions of two distinct Siwi complexes assembled during PIWI-interacting RNA biogenesis in Bombyx germ cells. Cell Rep. 10, 193–203 (2015).

    CAS  PubMed  Google Scholar 

  313. Kuramochi-Miyagawa, S. et al. MVH in piRNA processing and gene silencing of retrotransposons. Genes Dev. 24, 887–892 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  314. Wenda, J. M. et al. Distinct roles of RNA helicases MVH and TDRD9 in PIWI slicing-triggered mammalian piRNA biogenesis and function. Dev. Cell 41, 623–637 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  315. Pan, J. et al. RNF17, a component of the mammalian germ cell nuage, is essential for spermiogenesis. Development 132, 4029–4039 (2005).

    CAS  PubMed  Google Scholar 

  316. Zhang, Z. et al. Antisense piRNA amplification, but not piRNA production or nuage assembly, requires the Tudor-domain protein Qin. EMBO J. 33, 536–539 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  317. Wasik, K. A. et al. RNF17 blocks promiscuous activity of PIWI proteins in mouse testes. Genes Dev. 29, 1403–1415 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  318. Smith, J. M., Bowles, J., Wilson, M., Teasdale, R. D. & Koopman, P. Expression of the tudor-related gene Tdrd5 during development of the male germline in mice. Gene Expr. Patterns 4, 701–705 (2004).

    CAS  PubMed  Google Scholar 

  319. Yabuta, Y. et al. TDRD5 is required for retrotransposon silencing, chromatoid body assembly, and spermiogenesis in mice. J. Cell Biol. 192, 781–795 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  320. Ding, D. et al. TDRD5 binds piRNA precursors and selectively enhances pachytene piRNA processing in mice. Nat. Commun. 9, 127 (2018).

    PubMed  PubMed Central  Google Scholar 

  321. Hosokawa, M. et al. Tudor-related proteins TDRD1/MTR-1, TDRD6 and TDRD7/TRAP: domain composition, intracellular localization, and function in male germ cells in mice. Dev. Biol. 301, 38–52 (2007).

    CAS  PubMed  Google Scholar 

  322. Patil, V. S., Anand, A., Chakrabarti, A. & Kai, T. The Tudor domain protein Tapas, a homolog of the vertebrate Tdrd7, functions in piRNA pathway to regulate retrotransposons in germline of Drosophila melanogaster. BMC Biol. 12, 61 (2014).

    PubMed  PubMed Central  Google Scholar 

  323. Tanaka, T. et al. Tudor domain containing 7 (Tdrd7) is essential for dynamic ribonucleoprotein (RNP) remodeling of chromatoid bodies during spermatogenesis. Proc. Natl Acad. Sci. USA 108, 10579–10584 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  324. Zamparini, A. L. et al. Vreteno, a gonad-specific protein, is essential for germline development and primary piRNA biogenesis in Drosophila. Development 138, 4039–4050 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  325. Mathioudakis, N. et al. The multiple Tudor domain-containing protein TDRD1 is a molecular scaffold for mouse Piwi proteins and piRNA biogenesis factors. RNA 18, 2056–2072 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  326. Vasileva, A., Tiedau, D., Firooznia, A., Muller-Reichert, T. & Jessberger, R. Tdrd6 is required for spermiogenesis, chromatoid body architecture, and regulation of miRNA expression. Curr. Biol. 19, 630–639 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  327. Pandey, R. R. et al. Tudor domain containing 12 (TDRD12) is essential for secondary PIWI interacting RNA biogenesis in mice. Proc. Natl Acad. Sci. USA 110, 16492–16497 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  328. Xiol, J. et al. A role for Fkbp6 and the chaperone machinery in piRNA amplification and transposon silencing. Mol. Cell 47, 970–979 (2012).

    CAS  PubMed  Google Scholar 

  329. Preall, J. B., Czech, B., Guzzardo, P. M., Muerdter, F. & Hannon, G. J. shutdown is a component of the Drosophila piRNA biogenesis machinery. RNA 18, 1446–1457 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  330. Olivieri, D., Senti, K. A., Subramanian, S., Sachidanandam, R. & Brennecke, J. The cochaperone shutdown defines a group of biogenesis factors essential for all piRNA populations in Drosophila. Mol. Cell 47, 954–969 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  331. Specchia, V. et al. Hsp90 prevents phenotypic variation by suppressing the mutagenic activity of transposons. Nature 463, 662–665 (2010).

    CAS  PubMed  Google Scholar 

  332. Liu, L., Qi, H., Wang, J. & Lin, H. PAPI, a novel TUDOR-domain protein, complexes with AGO3, ME31B and TRAL in the nuage to silence transposition. Development 138, 1863–1873 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The authors thank J. Brennecke, W. Tang and members of the Zamore laboratory for discussions and critical comments on the manuscript.

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Nature Reviews Genetics thanks A. Kalmykova, R. Ketting and H. Siomi for their contribution to the peer review of this work.

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D.M.O., I.G. and A.Z. researched content for the article. All authors contributed to discussing the content, writing the manuscript, and reviewing or editing the manuscript before submission.

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Correspondence to Phillip D. Zamore.

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Glossary

Spermatogonial

Related to spermatogonia, which are the undifferentiated germ cells located at the periphery of seminiferous tubules. They undergo mitosis and later give rise to developing spermatocytes.

Heterochromatic

Consisting of heterochromatin, the tightly packed form of DNA whose histones are heavily modified with repressive marks, typically histone H3 lysine 9 trimethylation (H3K9me3).

Canonical transcription

This standard transcription requires a promoter (typically marked by histone H3 lysine 4 trimethylation (H3K4me3)) and generates RNA with a 5ʹ 7-methylguanosine cap and a 3ʹ poly(A) tail.

Pachytene

The stage of meiotic prophase I when homologous recombination occurs.

Initiator piRNA

A PIWI-interacting RNA (piRNA) that guides a PIWI protein to slice a piRNA precursor transcript, triggering production of responder and trailing piRNAs from it.

Pre-pre-piRNA

A 5ʹ monophosphorylated long RNA created by an initiator PIWI-interacting RNA (piRNA)-guided PIWI-catalysed slicing of a piRNA precursor transcript.

Responder piRNA

A PIWI-interacting RNA (piRNA) whose 5ʹ end is generated by initiator piRNA-guided PIWI-catalysed slicing of a piRNA precursor transcript.

Pre-piRNA

The intermediate product of PIWI-interacting RNA (piRNA) biogenesis loaded into a PIWI protein. Pre-piRNAs are 3ʹ-to-5ʹ trimmed and 2ʹ-O-methylated at their 3ʹ termini to yield mature piRNAs.

Trailing pre-piRNAs

A string of tail-to-head, phased trailing pre-piRNAs follows a responder piRNA. Both 5ʹ and 3ʹ ends of trailing piRNAs are made by the stepwise endonucleolytic fragmentation of a piRNA precursor transcript.

k cat

In Michaelis–Menten enzyme kinetics, the catalytic constant kcat represents the maximum number of substrate molecules converted to product per active site per unit time.

PIWI slicer activity

Endonucleolytic cleavage of the target RNA catalysed by PIWI-interacting RNA (piRNA)-guided PIWI proteins.

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Ozata, D.M., Gainetdinov, I., Zoch, A. et al. PIWI-interacting RNAs: small RNAs with big functions. Nat Rev Genet 20, 89–108 (2019). https://doi.org/10.1038/s41576-018-0073-3

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